comparison GEMBASSY-1.0.3/doc/text/gcbi.txt @ 0:8300eb051bea draft

Initial upload

0:8300eb051bea

                                      gcbi
Function

   Calculates the codon bias index (CBI)

Description

   gcbi calculates the codon bias index (CBI) for each gene af the given
   genome. CBI is a directional codon bias which measures the usage of
   optimal codons in a gene. CBI is similar to Fop, basically taking values
   from 0 (no bias) and 1 (maximum bias) and can take negative values
   depending on the codon usage.
    
   G-language SOAP service is provided by the
   Institute for Advanced Biosciences, Keio University.
   The original web service is located at the following URL:

   http://www.g-language.org/wiki/soap

   WSDL(RPC/Encoded) file is located at:

   http://soap.g-language.org/g-language.wsdl

   Documentation on G-language Genome Analysis Environment methods are
   provided at the Document Center

   http://ws.g-language.org/gdoc/

Usage

Here is a sample session with gcbi

% gcbi refseqn:NC_000913
Calculates the codon bias index (CBI)
Codon usage output file [nc_000913.gcbi]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.gcbi] Codon usage output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -translate          boolean    [N] Include when translating using standard
                                  codon table
   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
                                  expression to delete key (Any string)
   -[no]accid          boolean    [Y] Include to use sequence accession ID as
                                  query

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

   The database definitions for following commands are available at
   http://soap.g-language.org/kbws/embossrc

   gcbi reads one or more nucleotide sequences.

Output file format

   The output from gcbi is to a plain text file.

   File: nc_000913.gcbi

Sequence: NC_000913
cbi,gene
0.8716,thrL
0.3441,thrA
0.3462,thrB
0.4280,thrC
0.3868,yaaX
0.3908,yaaA
0.3521,yaaJ
0.5354,talB

   [Part of this file has been deleted for brevity]

0.4005,yjjX
0.4388,ytjC
0.3934,rob
0.4645,creA
0.4266,creB
0.3435,creC
0.3796,creD
0.4980,arcA
0.5412,yjjY
0.4018,yjtD


Data files

   None.

Notes

   None.

References

   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
      usage bias, J Mol Evol, 47(3):268-74.

   Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the
      psb A locus based on tRNA availability, J.Mol.Evo,. 37:273-280.

   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.

   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
      large-scale analysis of high-throughput omics data, J. Pest Sci.,
      31, 7.

   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
      Analysis Environment with REST and SOAP Web Service Interfaces,
      Nucleic Acids Res., 38, W700-W705.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   gdeltaenc Calculate the codon usage bias related to translation optimization
             (delta ENC)
   gicdi     Calculates the intrinsic codon deviation index (ICDI)
   gsvalue   Calculate the strength of selected codon usage bias (S)

Author(s)

   Hidetoshi Itaya ([e-mail])
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

   Kazuharu Arakawa ([e-mail])
   Institute for Advanced Biosciences, Keio University
   252-0882 Japan

History

   2012 - Written by Hidetoshi Itaya
   2013 - Fixed by Hidetoshi Itaya

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None.